User: Vitis

gravatar for Vitis
Vitis1.7k
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7 years, 5 months ago
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A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 220 results • page 1 of 22 • next >
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Meaning of the 5th column in repeatmasker BED format results
... I'd like to ask about the meaning of the 5th column (an integer number) in BED format results from repeatmasker. 9 100663131 100663387 LTR22_SS 475 + 9 70254161 70254685 ALTR2B_SSc 3460 + 9 96468811 96469391 LTR8_SSc 3756 - 9 116391614 116392469 LTR78 1152 + 9 4980341 4980930 L ...
genome written 1 day ago by Vitis1.7k • updated 1 day ago by Alex Reynolds26k
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Comment: C: Annotate VCF on specific transcripts (ANN field)
... Just a thought: maybe a custom GFF3 with just the gene/transcripts needed could be created and imported as a custom annotation database into snpEff. Then the annotation could be run against that database, which would probably save time, too. ...
written 9 days ago by Vitis1.7k
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Answer: A: Making BAM or SAM files equivalent
... Maybe bedtools multicov is something to try. Do sliding windows coverage comparisons across multiple BAMs, then you'll identify regions with comparable coverage across all samples. https://bedtools.readthedocs.io/en/latest/content/tools/multicov.html ...
written 14 days ago by Vitis1.7k
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Comment: C: Gene cluster visualization
... Adobe Illustrator, or any vector-based drawing tools, could do it. Just fit the pixels/arrow sizes to the gene scale in bp. ...
written 14 days ago by Vitis1.7k
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Comment: C: bedtools multicov - tab-delimited bam files?
... Looks like the error message is not referring to the BAM files but the input BED file specifying the interval/loci for coverage calculation. Can you post the first few lines of the input BED file? ...
written 14 days ago by Vitis1.7k
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Answer: A: How can I tell if there is CNV for specific gene in IGV?
... If you are using Illumina data for CNV discovery, there usually are two things you'll be looking for: coverage changes and breakpoints. Clean and clear-cut copy number changes are easy to spot on a coverage plot with distinct breakpoints from IGV or any other genome browser that supports BAM coverag ...
written 14 days ago by Vitis1.7k
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Answer: A: Need help to separate a genome in different x coverage
... If you're downsampling the WGS experiment across entire genome, simple `samtools view -s` would do it. Just be careful with using different seeds each time if you're doing repetitive subsampling, otherwise each time would generate the exact same subsample. ...
written 5 weeks ago by Vitis1.7k
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... 10X blocks only phases within the limits of 10X linked reads, if you need to go beyond the limits, you still need tools to bridge the 10X phased blocks. In Whatshap paper https://www.biorxiv.org/content/biorxiv/early/2016/11/14/085050.full.pdf It explicitly stats: > Instead of BAM, phasing inf ...
written 5 weeks ago by Vitis1.7k
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Answer: A: Depth of Coverage without Read Overlap
... According to this post https://www.biostars.org/p/87299/ "samtools mpileup", after version 1.X, doesn't double-count the overlapping read pairs. I don't know the default behavior of "samtools depth", but maybe a small test could be set up to see. ...
written 5 weeks ago by Vitis1.7k
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Answer: A: Is there a tool or method for phasing a VCF based on an already phased BAM?
... Whatshap is designed for this. It works a bit differently, requiring a solid, accurate VCF with variants to phase and a BAM (not phased), best from long-read technologies. https://whatshap.readthedocs.io/en/latest/ ...
written 5 weeks ago by Vitis1.7k

Latest awards to Vitis

Scholar 4 weeks ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Great Question 22 months ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 23 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Autobiographer 4.7 years ago, has more than 80 characters in the information field of the user's profile.
Guru 4.7 years ago, received more than 100 upvotes.
Centurion 4.7 years ago, created 100 posts.
Supporter 4.7 years ago, voted at least 25 times.
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Appreciated 6.7 years ago, created a post with more than 5 votes. For A: Rna-Seq Data Variant Calling
Teacher 6.7 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Data Variant Calling
Student 6.7 years ago, asked a question with at least 3 up-votes. For Genomic Read Mapping Biased Towards Coding Regions?
Appreciated 6.9 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Teacher 6.9 years ago, created an answer with at least 3 up-votes. For A: How To Convert Centimorgan To Base Pair
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: A Result From Mummer Alignment
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: What Are The 'Copy Number Detection' Tools Out There For Exome Capture Ngs Data.
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Time Course Data
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count

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